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Regular version of the site

Quality of Algorithms for Sequence Comparison

Abstract

Pair-wise sequence alignment is the basic method of comparative
analysis of proteins and nucleic acids. Studying the results of
the alignment one has to consider two questions: (1) did the program
find all the interesting similarities (sensitivity) and (2) are all the found
similarities interesting (selectivity). Definitely, one has to specify, what
alignments are considered as the interesting ones. Analogous questions
can be addressed to each of the obtained alignments: (3) which part
of the aligned positions are aligned correctly (confidence) and (4) does
alignment contain all pairs of the corresponding positions of compared
sequences (accuracy). Naturally, the answer on the questions depends on
the definition of the correct alignment. The presentation addresses the
above two pairs of questions that are extremely important in interpreting
of the results of sequence comparison.